Global analysis of autocorrelation functions and photon counting distributions

Frontiers in Bioscience - Elite

Volumn 3 E, Issue 2, 2011, Pages 489-505

  Skakun, Victor V ^a   Engel, Ruchira ^b   Digris, Anatoli V ^a   Borst, Jan Willem ^c   Visser, Antonie J W G ^c  

^a BELARUSIAN STATE UNIVERSITY   (Belarus)

^b UNIVERSITY OF LEEDS   (United Kingdom)

^c WAGENINGEN UNIVERSITY   (Netherlands)

Author keywords

Fluorescence Correlation Spectroscopy; Fluorescence Fluctuation Spectroscopy; Fluorescence Intensity Distribution Analysis; Global Analysis; Green Fluorescent Protein; Photon Counting Histogram

Indexed keywords

ARTICLE; BRIGHTNESS; DIFFUSION; FLUORESCENCE; FLUORESCENCE CORRELATION SPECTROSCOPY; HISTOGRAM; MATHEMATICAL ANALYSIS; PHOTON; PHOTON COUNTING HISTOGRAM ANALYSIS; COMPUTER PROGRAM; DIMERIZATION; METABOLISM; METHODOLOGY; OPTICS; SPECTROFLUOROMETRY; THEORETICAL MODEL; TIME;

ENHANCED GREEN FLUORESCENT PROTEIN; GREEN FLUORESCENT PROTEIN;

DIMERIZATION; GREEN FLUORESCENT PROTEINS; MODELS, THEORETICAL; OPTICS AND PHOTONICS; PHOTONS; SOFTWARE; SPECTROMETRY, FLUORESCENCE; TIME FACTORS;

EID: 79956200359     PISSN: 19450494     EISSN: 19450508     Source Type: Journal    
DOI: 10.2741/e264     Document Type: Article

References (77)

1. D. Magde, E. Elson and W. W. Webb: Thermodynamic fluctuations in a reaction system: Measurement by fluorescence correlation spectroscopy. Phys. Rev. Letters, 29(11), 705-708 (1972)
2. E. L. Elson and D. Magde: Fluorescence correlation spectroscopy. I Conceptual basis and theory. Biopolymers, 13, 1-27 (1974)
3. D. Magde, E. L. Elson and W. W. Webb: Fluorescence correlation spectroscopy. II. An experimental realization. Biopolymers, 13(1), 29-61 (1974)
4. N. L. Thompson: Fluorescence correlation spectroscopy. In: Topics in Fluorescence Spectroscopy. Ed J. R. Lakowicz. Plenum Press, New York, Vol. 1, 337-378 (1991)
5. R. Rigler, U. Mets, J. Widengren and P. Kask: Fluorescence correlation spectroscopy with high count rate and low background: Analysis of translational diffusion. Eur. Biophys. J., 22, 169-175 (1993) (Pubitemid 23279495)
6. M. Eigen and R. Rigler: Sorting single molecules: application to diagnostics and evolutionary biotechnology. Proc Natl Acad Sci U S A, 91(13), 5740-7 (1994) (Pubitemid 24188218)
7. K. M. Berland, P. T. So and E. Gratton: Two-photon fluorescence correlation spectroscopy: method and application to the intracellular environment. Biophys J, 68(2), 694-701 (1995)
8. K. M. Berland, P. T. So, Y. Chen, W. W. Mantulin and E. Gratton: Scanning two-photon fluctuation correlation spectroscopy: particle counting measurements for detection of molecular aggregation. Biophys J, 71(1), 410-20 (1996) (Pubitemid 26227327)
9. K. M. Berland: Fluorescence correlation spectroscopy: New methods for detecting molecular associations. Biophys. J., 72(4), 1487-1488 (1997)
10. S. Maiti, U. Haupts and W. W. Webb: Fluorescence correlation spectroscopy: diagnostics for sparse molecules. Proc Natl Acad Sci U S A, 94(22), 11753-7 (1997) (Pubitemid 27467786)
11. N. L. Thompson, A. M. Lieto and N. W. Allen: Recent advances in fluorescence correlation spectroscopy. Curr. Opin. Struct. Biol., 12(5), 634-41 (2002) (Pubitemid 35449072)
12. K. Bacia, S. A. Kim and P. Schwille: Fluorescence crosscorrelation spectroscopy in living cells. Nature Methods, 3(2), 83-89 (2006) (Pubitemid 43173305)
13. E. Haustein and P. Schwille: Fluorescence correlation spectroscopy: Novel variations of an established technique. Annu. Rev. Biophys. Biomol. Struct., 36, 151-169 (2007) (Pubitemid 46998114)
14. W. Al-Soufi, B. Reija , S. Felekyan, C. A. M. Seidel and M. Novo: Dynamics of supramolecular association monitored by fluorescence correlation spectroscopy. ChemPhysChem, 9(13), 1819-1827 (2008)
15. R. Rigler and E. S. Elson (Eds.): Fluorescence Correlation Spectroscopy. Theory and Applications. Springer, Berlin (2001)
16. S. T. Hess, S. Huang, A. A. Heikal and W. W. Webb: Biological and chemical applications of fluorescence correlation spectroscopy: a review. Biochemistry, 41(3), 697-705 (2002) (Pubitemid 34065283)
17. O. Krichevsky and G. Bonnet: Fluorescence correlation spectroscopy: the technique and its applications. Rep. Prog. Phys., 65, 251-297 (2002)
18. Y. Chen, J. D. Müller, P. T. So and E. Gratton: The photon counting histogram in fluorescence fluctuation spectroscopy. Biophys J, 77(1), 553-67 (1999) (Pubitemid 29305251)
19. Y. Chen, J. D. Müller, S. Y. Tetin, J. D. Tyner and E. Gratton: Probing ligand protein binding equilibria with fluorescence fluctuation spectroscopy. Biophys J, 79(2), 1074-84 (2000) (Pubitemid 30626198)
20. J. D. Müller, Y. Chen and E. Gratton: Resolving heterogeneity on the single molecular level with the photon-counting histogram. Biophys J, 78(1), 474-86 (2000) (Pubitemid 30207156)
21. Y. Chen, J. D. Müller, Q. Ruan and E. Gratton: Molecular brightness characterization of eGFP in vivo by fluorescence fluctuation spectroscopy. Biophys. J., 82, 133-144 (2002) (Pubitemid 34289788)
22. Y. Chen, L.-N. Wei and J. D. Müller: Probing protein oligomerization in living cells with fluorescence fluctuation spectroscopy. Proc. Natl. Acad. Sci. USA, 100(26), 15492-15497 (2003) (Pubitemid 38021017)
23. P. Kask, K. Palo, D. Ullmann and K. Gall: Fluorescenceintensity distribution analysis and its application in biomolecular detection technology. Proc. Natl. Acad. Sci. USA, 96(24), 13756-13761 (1999)
24. P. Kask, K. Palo, N. Fay, L. Brand, U. Mets, D. Ullmann, J. Jungmann, J. Pschorr and K. Gall: Two-dimensional fluorescence intensity distribution analysis: Theory and applications. Biophys. J., 78(4), 1703-1713 (2000) (Pubitemid 30183569)
25. K. Palo, U. Metz, S. Jager, P. Kask and K. Gall: Fluorescence intensity multiple distributions analysis: Concurrent determination of diffusion times and molecular brightness. Biophys. J., 79(6), 2858-2866 (2000)
26. K. Palo, U. Mets, V. Loorits and P. Kask: Calculation of photon count number distributions via master equations. Biophys. J., 90, 2179-2191 (2006)
27. F. Meng and H. Ma: A comparison between photon counting histogram and fluorescence intensity distribution analysis. J. Phys. Chem. B, 110(51), 25716-25720 (2006) (Pubitemid 46133280)
28. T. Kogure, S. Karasawa, T. Araki, K. Saito, M. Kinjo and A. Miyawaki: A fluorescent variant of a protein from the stony coral Montipora facilitates dual-color single-laser fluorescence cross-correlation spectroscopy. Nat Biotechnol, 24(5), 577-81 (2006)
29. P. Liu, T. Sudhaharan, R. M. Koh, L. C. Hwang, S. Ahmed, I. N. Maruyama and T. Wohland: Investigation of the dimerization of proteins from the epidermal growth factor receptor family by single wavelength fluorescence cross-correlation spectroscopy. Biophys J, 93(2), 684-98 (2007) (Pubitemid 47057833)
30. T. Rosales, V. Georget, D. Malide, A. Smirnov, J. Xu, C. Combs, J. R. Knutson, J. C. Nicolas and C. A. Royer: Quantitative detection of the ligand-dependent interaction between the androgen receptor and the co-activator, Tif2, in live cells using two color, two photon fluorescence crosscorrelation spectroscopy. Eur. Biophys. J., 36, 153-161 (2007) (Pubitemid 46175654)
31. M. A. Hink, K. Shah, E. Russinova, S. C. de Vries and A. J. W. G. Visser: Fluorescence fluctuation analysis of Arabidopsis thaliana somatic embryogenesis receptor-like kinase and brassinosteroid insensitive 1 receptor oligomerization. Biophys. J., 94(3), 1052-1062 (2008) (Pubitemid 351162468)
32. G. Vamosi, N. Baudendistel, C. W. von der Lieth, N. Szaloki, G. Mocsar, G. Muller, P. Brazda, W. Waldeck, S. Damjanovich, J. Langowski and K. Toth: Conformation of the c-Fos/c-Jun complex in vivo: a combined FRET, FCCS, and MD-modeling study. Biophys J, 94(7), 2859-68 (2008)
33. S. Zorrilla, A. Ortega, D. Chaix, C. Alfonso, G. Rivas, S. Aymerich, M. P. Lillo, N. Declerck and C. A. Royer: Characterization of the control catabolite protein of gluconeogenic genes repressor by fluorescence crosscorrelation spectroscopy and other biophysical approaches. Biophys J, 95(9), 4403-15 (2008)
34. T. Sudhaharan, P. Liu, Y. H. Foo, W. Bu, K. B. Lim, T. Wohland and S. Ahmed: Determination of in vivo dissociation constant, KD, of Cdc42-effector complexes in live mammalian cells using single wavelength fluorescence cross-correlation spectroscopy. J Biol Chem, 284(20), 13602-9 (2009)
35. Y. Chen, M. Tekmen, L. Hillesheim, J. Skinner, B. Wu and J. D. Müller: Dual-color photon-counting histogram. Biophys. J., 88(3), 2177-2192 (2005) (Pubitemid 40976226)
36. Y. Chen and J. D. Müller: Determining the stoichiometry of protein heterocomplexes in living cells with fluorescence fluctuation spectroscopy. Proc Natl Acad Sci U S A, 104(9), 3147-52 (2007) (Pubitemid 46364128)
37. T. Dertinger, V. Pacheco, I. von der Hocht, R. Hartmann, I. Gregor and J. Enderlein: Two-focus fluorescence correlation spectroscopy: a new tool for accurate and absolute diffusion measurements. ChemPhysChem, 8(3), 433-43 (2007)
38. Y. Korlann, T. Dertinger, X. Michalet, S. Weiss and J. Enderlein: Measuring diffusion with polarization-modulation dual-focus fluorescence correlation spectroscopy. Opt Express, 16(19), 14609-16 (2008)
39. A. Loman, T. Dertinger, F. Koberling and J. Enderlein: Comparison of optical saturation effects in conventional and dual-focus fluorescence correlation spectroscopy. Chem. Phys. Lett., 459(1-6), 18-21 (2008)
40. A. N. Kapanidis, N. K. Lee, T. A. Laurence, S. Doose, E. Margeat and S. Weiss: Fluorescence-aided molecule sorting: analysis of structure and interactions by alternating-laser excitation of single molecules. Proc Natl Acad Sci U S A, 101(24), 8936-41 (2004) (Pubitemid 38781589)
41. B. K. Müller, E. Zaychikov, C. Brauchle and D. C. Lamb: Pulsed interleaved excitation. Biophys J, 89(5), 3508-22 (2005) (Pubitemid 41636104)
42. G. Persson, P. Thyberg and J. Widengren: Modulated fluorescence correlation spectroscopy with complete time range information. Biophys J, 94(3), 977-85 (2008) (Pubitemid 351187688)
43. A. Benda, V. Fagul'ova, A. Deyneka, J. Enderlein and M. Hof: Fluorescence lifetime correlation spectroscopy combined with lifetime tuning: new perspectives in supported phospholipid bilayer research. Langmuir, 22(23), 9580-5 (2006) (Pubitemid 44826366)
44. J. Humpolickova, A. Benda, J. Sykora, R. Machan, T. Kral, B. Gasinska, J. Enderlein and M. Hof: Equilibrium dynamics of spermine-induced plasmid DNA condensation revealed by fluorescence lifetime correlation spectroscopy. Biophys J, 94(3), L17-9 (2008) (Pubitemid 351162440)
45. Z. Petrasek and P. Schwille: Precise measurement of diffusion coefficients using scanning fluorescence correlation spectroscopy. Biophys J, 94(4), 1437-48 (2008)
46. A. M. Lieto and N. L. Thompson: Total internal reflection with fluorescence correlation spectroscopy: Nonfluorescent competitors. Biophys. J., 87(2), 1268-1278 (2004) (Pubitemid 39095103)
47. K. Hassler, T. Anhut, R. Rigler, M. Gosch and T. Lasser: High count rates with total internal reflection fluorescence correlation spectroscopy. Biophys J, 88(1), L01-3 (2005) (Pubitemid 40070650)
48. Y. Ohsugi, K. Saito, M. Tamura and M. Kinjo: Lateral mobility of membrane-binding proteins in living cells measured by total internal reflection fluorescence correlation spectroscopy. Biophys J, 91(9), 3456-64 (2006)
49. N. L. Thompson and B. L. Steele: Total internal reflection with fluorescence correlation spectroscopy. Nat. Protocols, 2(4), 878-90 (2007) (Pubitemid 46745588)
50. D. L. Kolin and P. W. Wiseman: Advances in image correlation spectroscopy: Measuring number densities, aggregation states, and dynamics of fluorescently labeled macromolecules in cells. Cell Biochem. Biophys., 49(3), 141-164 (2007) (Pubitemid 350242576)
51. M. A. Digman, C. M. Brown, P. Sengupta, P. W. Wiseman, A. R. Horwitz and E. Gratton: Measuring fast dynamics in solutions and cells with a laser scanning microscope. Biophys. J., 89, 1317-1327 (2005) (Pubitemid 41099013)
52. M. A. Digman, P. Sengupta, P. W. Wiseman, C. M. Brown, A. R. Horwitz and E. Gratton: Fluctuation correlation spectroscopy with a laser-scanning microscope: exploiting the hidden time structure Biophys. J., 89, L33-L36 (2005) (Pubitemid 40586559)
53. M. A. Digman, P. W. Wiseman, A. R. Horwitz and E. Gratton: Detecting protein complexes in living cells from laser scanning confocal image sequences by the cross correlation raster image spectroscopy method. Biophys J, 96(2), 707-16 (2009)
54. S. T. Hess and W. W. Webb: Focal volume optics and experimental artifacts in confocal fluorescence correlation spectroscopy. Biophys. J., 83(4), 2300-2317 (2002)
55. L. N. Hillesheim and J. D. Müller: The photon counting histogram in fluorescence fluctuation spectroscopy with non-ideal photodetectors. Biophys. J., 85(3), 1948-1958 (2003) (Pubitemid 37052274)
56. J. Enderlein, I. Gregor, D. Patra, T. Dertinger and U. B. Kaupp: Performance of fluorescence correlation spectroscopy for measuring diffusion and concentration. ChemPhysChem, 6(11), 2324-36 (2005) (Pubitemid 41641717)
57. I. Gregor, D. Patra and J. Enderlein: Optical saturation in fluorescence correlation spectroscopy under continuous-wave and pulsed excitation. ChemPhysChem, 6(1), 164-70 (2005) (Pubitemid 40203550)
58. T. D. Perroud, B. Huang, M. I. Wallace and R. N. Zare: Photon counting histogram for one-photon excitation. ChemPhysChem, 4(10), 1121-1123 (2003)
59. B. Huang, T. D. Perroud and R. N. Zare: Photon counting histogram: One-photon excitation. ChemPhysChem, 5, 1523-1531 (2004)
60. T. D. Perroud, B. Huang and R. N. Zare: Effect of bin time on the photon counting histogram for onephoton excitation. ChemPhysChem, 6(5), 905-912 (2005) (Pubitemid 40669556)
61. V. V. Skakun, M. A. Hink, A. V. Digris, R. Engel, E. G. Novikov, V. V. Apanasovich and A. J. Visser: Global analysis of fluorescence fluctuation data. Eur Biophys J, 34(4), 323-34 (2005) (Pubitemid 40884077)
62. J. D. Müller. Cumulant analysis in fluctuation spectroscopy. Biophys J, 86, 3981-3992 (2004)
63. I. Shingaryov, V. V. Skakun and V. V. Apanasovich: Photon counts simulation in fluorescence fluctuation spectroscopy. In: Pattern Recognition and Information Processing. Eds. V. Krasnoproshin et al., Publ. center of BSU, Minsk, 178-182 (2009)
64. I. V. Gopich and A. Szabo: Photon counting histograms for diffusive fluorophores. J. Phys. Chem. B, 109, 17683-17688 (2005) (Pubitemid 41396219)
65. E. Novikov and N. Boens: Analytical model of the fluorescence fluctuation spectroscopy experiment. J. Chem. Phys., 114, 1745-1753 (2001) (Pubitemid 32168684)
66. P. R. Bevington and D. K. Robinson: Data Reduction and Error Analysis for the Physical Sciences. McGraw-Hill, New York (2003)
67. T. Wohland, R. Rigler and H. Vogel: The standard deviation in fluorescence correlation spectroscopy. Biophys. J., 80, 2987-2999 (2001) (Pubitemid 32521670)
68. A. J. W. G. Visser, S. P. Laptenok, N. V. Visser, A. van Hoek, D. J. S. Birch, J. C. Brochon and J. W. Borst: Timeresolved FRET fluorescence spectroscopy of visible fluorescent protein pairs. Eur. Biophys. J., 39, 241-253 (2010)
69. M. A. Hink, J. W. Borst and A. J. W. G. Visser: Fluorescence correlation spectroscopy of GFP fusion proteins in living plant cells. Methods Enzymol., 361, 93-112 (2003) (Pubitemid 36244916)
70. K. Weisshart, V. Jüngel and S. J. Briddon: The LSM 510 META - ConfoCor 2 system: An integrated imaging and spectroscopic platform for single-molecule detection. Curr. Pharm. Biotechnol., 5, 135-154 (2004) (Pubitemid 38594435)
71. J. Widengren, U. Mets and R. Rigler: Fluorescence correlation spectroscopy of triplet states in solution: A theoretical and experimental study. J. Phys. Chem., 99, 13368-13379 (1995)
72. J. M. Beechem, E. Gratton, M. Ameloot, J. R. Knutson and L. Brand: Analysis of fluorescence intensity and anisotropy decay data: Second generation theory and programs. In: Topics in Fluorescence Spectroscopy. Ed. J. R. Lakowicz. Plenum Press, New York, Vol. 2, 241-305 (1991)
73. M. L. Johnson and L. M. Faunt: Parameter estimation by least-squares methods. Methods Enzymol., 210, 1-37 (1992)
74. V.V. Skakun, E.G. Novikov, V.V. Apanasovich, H.J. Tanke, A.M. Deelder, O.A. Mayboroda: Initial Guesses Generation for Fluorescence Intensity Distribution Analysis. Eur. Biophys. J. 35(5), 410-423 (2006)
75. H.T. Lau: A Numerical Library in C for Scientists and Engineers. CRC Press, Boca Raton (1995)
76. W.H. Press, S.A. Teukolsky, W.T. Vetterling, B.P. Flannery: Numerical Recipes in C. The art of scientific computing. 2nd ed. Cambridge University Press, Cambridge (1992)
77. N. Dross, C. Spriet, M. Zwerger, G. Muller, W. Waldeck and J. Langowski: Mapping eGFP oligomer mobility in living cell nuclei. PLoS One, 4(4), e5041 (2009)